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- PDB-5h5c: Mdm12 from K. lactis (1-239), uniformly Lys dimethyl modified, cr... -

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Basic information

Entry
Database: PDB / ID: 5h5c
TitleMdm12 from K. lactis (1-239), uniformly Lys dimethyl modified, crystallized in FOS-MEA-10
ComponentsMitochondrial distribution and morphology protein 12
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


ERMES complex / mitochondrial genome maintenance / lipid transport / protein insertion into mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane
Similarity search - Function
MMM1 domain / Maintenance of mitochondrial morphology protein 1 / Mitochondrial distribution and morphology protein 12 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile.
Similarity search - Domain/homology
Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsKawano, S. / Quinbara, S. / Endo, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25840020 Japan
CitationJournal: J. Cell Biol. / Year: 2018
Title: Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES
Authors: Kawano, S. / Tamura, Y. / Kojima, R. / Bala, S. / Asai, E. / Michel, A.H. / Kornmann, B. / Riezman, I. / Riezman, H. / Sakae, Y. / Okamoto, Y. / Endo, T.
History
DepositionNov 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)27,4661
Polymers27,4661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10900 Å2
2
A: Mitochondrial distribution and morphology protein 12

A: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)54,9332
Polymers54,9332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
Buried area1680 Å2
ΔGint-16 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.391, 93.391, 81.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Mitochondrial distribution and morphology protein 12 / Mitochondrial inheritance component MDM12


Mass: 27466.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: MDM12, KLLA0C06028g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CUC3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.26M NaH2PO4 0.14M K2HPO4 pH5.6 0.55mM FOS-MEA-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.31→50 Å / Num. obs: 535031 / % possible obs: 99.6 % / Redundancy: 10.7 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→50 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.824 / SU B: 0.019 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.554 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33512 295 4.6 %RANDOM
Rwork0.29641 ---
obs0.29826 6065 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å2-0 Å2
2--0.45 Å20 Å2
3----1.45 Å2
Refinement stepCycle: 1 / Resolution: 3.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 0 1458
LS refinement shellResolution: 3.312→3.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 21 -
Rwork0.334 457 -
obs--98.76 %

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